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ArrayIndexOutOfBoundsException
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Trevor

Joined: 19 Mar 2001
Posts: 123

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Link to postPosted: Thu May 10, 2007 3:54 amPost subject: ArrayIndexOutOfBoundsException Reply with quote

We see this error in our logs a lot - I don't have an example molecule to duplicate it however.

java.lang.ArrayIndexOutOfBoundsException: 6
at chemaxon.calculations.pKa.getNitrogenBasicType(pKa.java:8356)
at chemaxon.calculations.pKa.setBasicAtoms(pKa.java:8178)
at chemaxon.calculations.pKa.getApKa(pKa.java:839)
at chemaxon.calculations.pKa.getAcidicpKa(pKa.java:138)
at chemaxon.calculations.Ionizer.initMicropk0(Ionizer.java:1175)
at chemaxon.calculations.Ionizer.calcStartValues(Ionizer.java:1134)
at chemaxon.calculations.Ionizer.initMsCalculation(Ionizer.java:1083)
at chemaxon.calculations.Ionizer.calcMicroSpecies(Ionizer.java:419)
at chemaxon.calculations.Ionizer.calculatepKa(Ionizer.java:1898)
at chemaxon.calculations.Ionizer.calculatepKa(Ionizer.java:1884)
at chemaxon.marvin.calculations.pKaPlugin.run(pKaPlugin.java:435)
Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

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Link to postPosted: Mon May 14, 2007 10:03 amPost subject: Reply with quote

Hi,

What version of Marvin/JChem are you running?

Best regards,
Zsolt
Trevor

Joined: 19 Mar 2001
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Link to postPosted: Mon May 14, 2007 3:43 pmPost subject: Reply with quote

jchem 3.2.5
Tamas
ChemAxon personnel
Joined: 21 May 2004
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Link to postPosted: Wed May 16, 2007 8:52 pmPost subject: Reply with quote

Thanks the info. We are checking it.
Jozsef
ChemAxon personnel
Joined: 25 May 2004
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Link to postPosted: Thu May 17, 2007 9:22 amPost subject: Reply with quote

Hi,

From the exception message you have sent it seems to me you are using an older version of JChem.

Are you sure you are using JChem 3.2.5?

This bug has already been fixed, and it should work in JChem 3.2.5. We have tested the pKa module on a large data set, and we haven't got any "ArrayIndexOutOfBoundsException” messages.

Jozsi
Jozsef
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Joined: 25 May 2004
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Link to postPosted: Thu May 17, 2007 10:10 amPost subject: Reply with quote

Hi,


May be the "java.lang.ArrayIndexOutOfBoundsException: 6...." message that you obtained from a logs file was created with an older JChem.
Is it possible?

Jozsi
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